HEADER HYDROLASE 13-DEC-17 6F8T TITLE CRYSTAL STRUCTURE OF THE PDE4D CATALYTIC DOMAIN IN COMPLEX WITH GEBR- TITLE 2 4A COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAMP-SPECIFIC 3',5'-CYCLIC PHOSPHODIESTERASE 4D; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DPDE3,PDE43; COMPND 5 EC: 3.1.4.53; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PDE4D, DPDE3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS PDE4, CATALYTIC DOMAIN, INHIBITOR, GEBR, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR T.PROSDOCIMI,S.DONINI,E.PARISINI REVDAT 3 17-JAN-24 6F8T 1 LINK REVDAT 2 23-MAY-18 6F8T 1 JRNL REVDAT 1 16-MAY-18 6F8T 0 JRNL AUTH T.PROSDOCIMI,L.MOLLICA,S.DONINI,M.S.SEMRAU,A.P.LUCARELLI, JRNL AUTH 2 E.AIOLFI,A.CAVALLI,P.STORICI,S.ALFEI,C.BRULLO,O.BRUNO, JRNL AUTH 3 E.PARISINI JRNL TITL MOLECULAR BASES OF PDE4D INHIBITION BY MEMORY-ENHANCING GEBR JRNL TITL 2 LIBRARY COMPOUNDS. JRNL REF BIOCHEMISTRY V. 57 2876 2018 JRNL REFN ISSN 1520-4995 JRNL PMID 29652483 JRNL DOI 10.1021/ACS.BIOCHEM.8B00288 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.63 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 71439 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 3615 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 45.6417 - 5.3298 1.00 2822 149 0.1691 0.1739 REMARK 3 2 5.3298 - 4.2314 1.00 2710 136 0.1487 0.1887 REMARK 3 3 4.2314 - 3.6968 1.00 2668 128 0.1546 0.1981 REMARK 3 4 3.6968 - 3.3589 1.00 2644 142 0.1687 0.1641 REMARK 3 5 3.3589 - 3.1182 1.00 2626 158 0.1713 0.2272 REMARK 3 6 3.1182 - 2.9344 1.00 2598 144 0.1768 0.2082 REMARK 3 7 2.9344 - 2.7874 1.00 2630 137 0.1747 0.2064 REMARK 3 8 2.7874 - 2.6661 1.00 2595 142 0.1766 0.2644 REMARK 3 9 2.6661 - 2.5635 1.00 2627 149 0.1713 0.1976 REMARK 3 10 2.5635 - 2.4750 1.00 2595 122 0.1685 0.1987 REMARK 3 11 2.4750 - 2.3977 1.00 2611 137 0.1707 0.2219 REMARK 3 12 2.3977 - 2.3291 1.00 2618 137 0.1709 0.2027 REMARK 3 13 2.3291 - 2.2678 1.00 2608 124 0.1717 0.2376 REMARK 3 14 2.2678 - 2.2125 1.00 2578 143 0.1719 0.2477 REMARK 3 15 2.2125 - 2.1622 1.00 2594 143 0.1736 0.2363 REMARK 3 16 2.1622 - 2.1162 1.00 2586 150 0.1752 0.2289 REMARK 3 17 2.1162 - 2.0738 1.00 2574 131 0.1798 0.2176 REMARK 3 18 2.0738 - 2.0347 1.00 2585 124 0.1718 0.2115 REMARK 3 19 2.0347 - 1.9984 1.00 2567 141 0.1852 0.2606 REMARK 3 20 1.9984 - 1.9645 1.00 2604 137 0.1791 0.2324 REMARK 3 21 1.9645 - 1.9328 1.00 2557 146 0.1853 0.2458 REMARK 3 22 1.9328 - 1.9031 1.00 2591 127 0.1831 0.2456 REMARK 3 23 1.9031 - 1.8751 1.00 2613 142 0.1941 0.2677 REMARK 3 24 1.8751 - 1.8487 0.99 2496 144 0.1902 0.2314 REMARK 3 25 1.8487 - 1.8237 1.00 2592 141 0.1925 0.2943 REMARK 3 26 1.8237 - 1.8000 0.99 2535 141 0.1965 0.2620 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.290 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 5519 REMARK 3 ANGLE : 0.947 7519 REMARK 3 CHIRALITY : 0.039 872 REMARK 3 PLANARITY : 0.004 961 REMARK 3 DIHEDRAL : 14.077 2052 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6F8T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-DEC-17. REMARK 100 THE DEPOSITION ID IS D_1200007766. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-JUN-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 71439 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 45.627 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.04500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.25 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 6F6U REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HEPES PEG 3350 MAGNESIUM CHLORIDE, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 32.26550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 59.81150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 49.35850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 59.81150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 32.26550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 49.35850 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2150 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28090 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -121.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 243 REMARK 465 SER A 244 REMARK 465 ILE A 245 REMARK 465 PRO A 246 REMARK 465 ARG A 247 REMARK 465 PHE A 248 REMARK 465 GLY A 249 REMARK 465 GLN A 578 REMARK 465 ALA A 579 REMARK 465 HIS A 580 REMARK 465 HIS A 581 REMARK 465 HIS A 582 REMARK 465 HIS A 583 REMARK 465 HIS A 584 REMARK 465 HIS A 585 REMARK 465 MET B 243 REMARK 465 SER B 244 REMARK 465 ILE B 245 REMARK 465 PRO B 246 REMARK 465 ARG B 247 REMARK 465 PHE B 248 REMARK 465 GLY B 249 REMARK 465 VAL B 250 REMARK 465 LYS B 251 REMARK 465 THR B 252 REMARK 465 GLU B 253 REMARK 465 GLN B 254 REMARK 465 GLU B 255 REMARK 465 HIS B 580 REMARK 465 HIS B 581 REMARK 465 HIS B 582 REMARK 465 HIS B 583 REMARK 465 HIS B 584 REMARK 465 HIS B 585 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 251 CG CD CE NZ REMARK 470 GLU A 253 CG CD OE1 OE2 REMARK 470 GLN A 254 CG CD OE1 NE2 REMARK 470 GLU A 255 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 707 O HOH A 840 1.99 REMARK 500 OD1 ASP B 511 NH2 ARG B 514 2.10 REMARK 500 OD1 ASP A 511 NH2 ARG A 514 2.11 REMARK 500 OE2 GLU A 504 NH2 ARG A 508 2.12 REMARK 500 O HOH B 875 O HOH B 981 2.13 REMARK 500 OG1 THR B 575 O HOH B 701 2.13 REMARK 500 OE1 GLU A 548 O HOH A 701 2.14 REMARK 500 OG SER A 392 O HOH A 702 2.14 REMARK 500 O HOH B 858 O HOH B 951 2.17 REMARK 500 NE2 GLN B 293 O HOH B 702 2.17 REMARK 500 O HOH A 980 O HOH A 993 2.18 REMARK 500 O HOH A 998 O HOH A 1008 2.18 REMARK 500 NH1 ARG A 472 O HOH A 703 2.19 REMARK 500 OD1 ASP A 306 O HOH A 704 2.19 REMARK 500 O HOH A 707 O HOH A 933 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 LYS A 251 -24.41 87.69 REMARK 500 GLU A 253 66.20 -62.72 REMARK 500 GLU A 255 -121.64 65.23 REMARK 500 ASP A 256 -94.35 -114.50 REMARK 500 VAL A 257 115.88 174.97 REMARK 500 LEU A 258 -52.23 91.85 REMARK 500 ASN A 327 -169.45 -125.59 REMARK 500 ILE A 542 -60.94 -122.09 REMARK 500 LEU B 258 -44.04 -147.08 REMARK 500 THR B 459 -177.10 -69.51 REMARK 500 ILE B 542 -59.23 -128.67 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 601 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 330 NE2 REMARK 620 2 HIS A 366 NE2 95.4 REMARK 620 3 ASP A 367 OD2 88.1 87.3 REMARK 620 4 ASP A 484 OD1 87.9 89.8 174.8 REMARK 620 5 HOH A 756 O 170.0 94.6 92.2 92.3 REMARK 620 6 HOH A 840 O 85.0 175.2 97.6 85.4 85.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 602 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 367 OD1 REMARK 620 2 HOH A 756 O 94.2 REMARK 620 3 HOH A 803 O 82.5 98.4 REMARK 620 4 HOH A 857 O 168.3 93.2 87.6 REMARK 620 5 HOH A 867 O 88.7 172.9 88.4 84.9 REMARK 620 6 HOH A 933 O 98.8 88.3 173.0 90.3 84.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 604 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 417 OD1 REMARK 620 2 HOH A 714 O 28.4 REMARK 620 3 HOH A 839 O 25.0 3.4 REMARK 620 4 HOH A 847 O 25.8 4.2 3.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 605 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 467 OD2 REMARK 620 2 ASP A 471 OD2 98.3 REMARK 620 3 HOH A 779 O 87.6 95.0 REMARK 620 4 HOH A 780 O 93.2 86.3 178.4 REMARK 620 5 HOH A 814 O 172.7 88.9 90.6 88.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 601 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 330 NE2 REMARK 620 2 HIS B 366 NE2 94.1 REMARK 620 3 ASP B 367 OD2 88.7 83.1 REMARK 620 4 ASP B 484 OD1 86.5 92.1 173.0 REMARK 620 5 HOH B 726 O 170.2 95.7 93.2 92.4 REMARK 620 6 HOH B 838 O 88.8 175.5 100.4 84.6 81.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 602 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 367 OD1 REMARK 620 2 HOH B 726 O 97.0 REMARK 620 3 HOH B 758 O 82.6 96.7 REMARK 620 4 HOH B 832 O 168.9 89.2 87.5 REMARK 620 5 HOH B 848 O 89.3 171.4 90.0 85.6 REMARK 620 6 HOH B 868 O 99.6 86.3 176.0 89.9 86.8 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 605 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CZT A 606 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CZT B 603 DBREF 6F8T A 244 578 UNP Q08499 PDE4D_HUMAN 244 578 DBREF 6F8T B 244 578 UNP Q08499 PDE4D_HUMAN 244 578 SEQADV 6F8T MET A 243 UNP Q08499 INITIATING METHIONINE SEQADV 6F8T ALA A 579 UNP Q08499 EXPRESSION TAG SEQADV 6F8T HIS A 580 UNP Q08499 EXPRESSION TAG SEQADV 6F8T HIS A 581 UNP Q08499 EXPRESSION TAG SEQADV 6F8T HIS A 582 UNP Q08499 EXPRESSION TAG SEQADV 6F8T HIS A 583 UNP Q08499 EXPRESSION TAG SEQADV 6F8T HIS A 584 UNP Q08499 EXPRESSION TAG SEQADV 6F8T HIS A 585 UNP Q08499 EXPRESSION TAG SEQADV 6F8T MET B 243 UNP Q08499 INITIATING METHIONINE SEQADV 6F8T ALA B 579 UNP Q08499 EXPRESSION TAG SEQADV 6F8T HIS B 580 UNP Q08499 EXPRESSION TAG SEQADV 6F8T HIS B 581 UNP Q08499 EXPRESSION TAG SEQADV 6F8T HIS B 582 UNP Q08499 EXPRESSION TAG SEQADV 6F8T HIS B 583 UNP Q08499 EXPRESSION TAG SEQADV 6F8T HIS B 584 UNP Q08499 EXPRESSION TAG SEQADV 6F8T HIS B 585 UNP Q08499 EXPRESSION TAG SEQRES 1 A 343 MET SER ILE PRO ARG PHE GLY VAL LYS THR GLU GLN GLU SEQRES 2 A 343 ASP VAL LEU ALA LYS GLU LEU GLU ASP VAL ASN LYS TRP SEQRES 3 A 343 GLY LEU HIS VAL PHE ARG ILE ALA GLU LEU SER GLY ASN SEQRES 4 A 343 ARG PRO LEU THR VAL ILE MET HIS THR ILE PHE GLN GLU SEQRES 5 A 343 ARG ASP LEU LEU LYS THR PHE LYS ILE PRO VAL ASP THR SEQRES 6 A 343 LEU ILE THR TYR LEU MET THR LEU GLU ASP HIS TYR HIS SEQRES 7 A 343 ALA ASP VAL ALA TYR HIS ASN ASN ILE HIS ALA ALA ASP SEQRES 8 A 343 VAL VAL GLN SER THR HIS VAL LEU LEU SER THR PRO ALA SEQRES 9 A 343 LEU GLU ALA VAL PHE THR ASP LEU GLU ILE LEU ALA ALA SEQRES 10 A 343 ILE PHE ALA SER ALA ILE HIS ASP VAL ASP HIS PRO GLY SEQRES 11 A 343 VAL SER ASN GLN PHE LEU ILE ASN THR ASN SER GLU LEU SEQRES 12 A 343 ALA LEU MET TYR ASN ASP SER SER VAL LEU GLU ASN HIS SEQRES 13 A 343 HIS LEU ALA VAL GLY PHE LYS LEU LEU GLN GLU GLU ASN SEQRES 14 A 343 CYS ASP ILE PHE GLN ASN LEU THR LYS LYS GLN ARG GLN SEQRES 15 A 343 SER LEU ARG LYS MET VAL ILE ASP ILE VAL LEU ALA THR SEQRES 16 A 343 ASP MET SER LYS HIS MET ASN LEU LEU ALA ASP LEU LYS SEQRES 17 A 343 THR MET VAL GLU THR LYS LYS VAL THR SER SER GLY VAL SEQRES 18 A 343 LEU LEU LEU ASP ASN TYR SER ASP ARG ILE GLN VAL LEU SEQRES 19 A 343 GLN ASN MET VAL HIS CYS ALA ASP LEU SER ASN PRO THR SEQRES 20 A 343 LYS PRO LEU GLN LEU TYR ARG GLN TRP THR ASP ARG ILE SEQRES 21 A 343 MET GLU GLU PHE PHE ARG GLN GLY ASP ARG GLU ARG GLU SEQRES 22 A 343 ARG GLY MET GLU ILE SER PRO MET CYS ASP LYS HIS ASN SEQRES 23 A 343 ALA SER VAL GLU LYS SER GLN VAL GLY PHE ILE ASP TYR SEQRES 24 A 343 ILE VAL HIS PRO LEU TRP GLU THR TRP ALA ASP LEU VAL SEQRES 25 A 343 HIS PRO ASP ALA GLN ASP ILE LEU ASP THR LEU GLU ASP SEQRES 26 A 343 ASN ARG GLU TRP TYR GLN SER THR ILE PRO GLN ALA HIS SEQRES 27 A 343 HIS HIS HIS HIS HIS SEQRES 1 B 343 MET SER ILE PRO ARG PHE GLY VAL LYS THR GLU GLN GLU SEQRES 2 B 343 ASP VAL LEU ALA LYS GLU LEU GLU ASP VAL ASN LYS TRP SEQRES 3 B 343 GLY LEU HIS VAL PHE ARG ILE ALA GLU LEU SER GLY ASN SEQRES 4 B 343 ARG PRO LEU THR VAL ILE MET HIS THR ILE PHE GLN GLU SEQRES 5 B 343 ARG ASP LEU LEU LYS THR PHE LYS ILE PRO VAL ASP THR SEQRES 6 B 343 LEU ILE THR TYR LEU MET THR LEU GLU ASP HIS TYR HIS SEQRES 7 B 343 ALA ASP VAL ALA TYR HIS ASN ASN ILE HIS ALA ALA ASP SEQRES 8 B 343 VAL VAL GLN SER THR HIS VAL LEU LEU SER THR PRO ALA SEQRES 9 B 343 LEU GLU ALA VAL PHE THR ASP LEU GLU ILE LEU ALA ALA SEQRES 10 B 343 ILE PHE ALA SER ALA ILE HIS ASP VAL ASP HIS PRO GLY SEQRES 11 B 343 VAL SER ASN GLN PHE LEU ILE ASN THR ASN SER GLU LEU SEQRES 12 B 343 ALA LEU MET TYR ASN ASP SER SER VAL LEU GLU ASN HIS SEQRES 13 B 343 HIS LEU ALA VAL GLY PHE LYS LEU LEU GLN GLU GLU ASN SEQRES 14 B 343 CYS ASP ILE PHE GLN ASN LEU THR LYS LYS GLN ARG GLN SEQRES 15 B 343 SER LEU ARG LYS MET VAL ILE ASP ILE VAL LEU ALA THR SEQRES 16 B 343 ASP MET SER LYS HIS MET ASN LEU LEU ALA ASP LEU LYS SEQRES 17 B 343 THR MET VAL GLU THR LYS LYS VAL THR SER SER GLY VAL SEQRES 18 B 343 LEU LEU LEU ASP ASN TYR SER ASP ARG ILE GLN VAL LEU SEQRES 19 B 343 GLN ASN MET VAL HIS CYS ALA ASP LEU SER ASN PRO THR SEQRES 20 B 343 LYS PRO LEU GLN LEU TYR ARG GLN TRP THR ASP ARG ILE SEQRES 21 B 343 MET GLU GLU PHE PHE ARG GLN GLY ASP ARG GLU ARG GLU SEQRES 22 B 343 ARG GLY MET GLU ILE SER PRO MET CYS ASP LYS HIS ASN SEQRES 23 B 343 ALA SER VAL GLU LYS SER GLN VAL GLY PHE ILE ASP TYR SEQRES 24 B 343 ILE VAL HIS PRO LEU TRP GLU THR TRP ALA ASP LEU VAL SEQRES 25 B 343 HIS PRO ASP ALA GLN ASP ILE LEU ASP THR LEU GLU ASP SEQRES 26 B 343 ASN ARG GLU TRP TYR GLN SER THR ILE PRO GLN ALA HIS SEQRES 27 B 343 HIS HIS HIS HIS HIS HET ZN A 601 1 HET MG A 602 1 HET MG A 603 1 HET MG A 604 1 HET MG A 605 1 HET CZT A 606 63 HET ZN B 601 1 HET MG B 602 1 HET CZT B 603 63 HETNAM ZN ZINC ION HETNAM MG MAGNESIUM ION HETNAM CZT (2~{R})-1-[(~{E})-(3-CYCLOPENTYLOXY-4-METHOXY-PHENYL) HETNAM 2 CZT METHYLIDENEAMINO]OXY-3-[(2~{R},6~{S})-2,6- HETNAM 3 CZT DIMETHYLMORPHOLIN-4-YL]PROPAN-2-OL FORMUL 3 ZN 2(ZN 2+) FORMUL 4 MG 5(MG 2+) FORMUL 8 CZT 2(C22 H34 N2 O5) FORMUL 12 HOH *624(H2 O) HELIX 1 AA1 LEU A 258 GLU A 263 1 6 HELIX 2 AA2 HIS A 271 SER A 279 1 9 HELIX 3 AA3 ARG A 282 ARG A 295 1 14 HELIX 4 AA4 ASP A 296 LYS A 302 1 7 HELIX 5 AA5 PRO A 304 HIS A 318 1 15 HELIX 6 AA6 ASN A 327 SER A 343 1 17 HELIX 7 AA7 THR A 344 GLU A 348 5 5 HELIX 8 AA8 THR A 352 HIS A 366 1 15 HELIX 9 AA9 SER A 374 THR A 381 1 8 HELIX 10 AB1 SER A 383 TYR A 389 1 7 HELIX 11 AB2 SER A 393 LEU A 406 1 14 HELIX 12 AB3 LEU A 407 GLU A 409 5 3 HELIX 13 AB4 THR A 419 ALA A 436 1 18 HELIX 14 AB5 THR A 437 SER A 440 5 4 HELIX 15 AB6 LYS A 441 THR A 455 1 15 HELIX 16 AB7 ASN A 468 LEU A 485 1 18 HELIX 17 AB8 SER A 486 LYS A 490 5 5 HELIX 18 AB9 PRO A 491 ARG A 516 1 26 HELIX 19 AC1 SER A 530 ILE A 542 1 13 HELIX 20 AC2 ILE A 542 VAL A 554 1 13 HELIX 21 AC3 ALA A 558 THR A 575 1 18 HELIX 22 AC4 LYS B 260 VAL B 265 5 6 HELIX 23 AC5 HIS B 271 SER B 279 1 9 HELIX 24 AC6 ARG B 282 ARG B 295 1 14 HELIX 25 AC7 ASP B 296 PHE B 301 1 6 HELIX 26 AC8 PRO B 304 HIS B 318 1 15 HELIX 27 AC9 ASN B 327 SER B 343 1 17 HELIX 28 AD1 THR B 344 GLU B 348 5 5 HELIX 29 AD2 THR B 352 HIS B 366 1 15 HELIX 30 AD3 SER B 374 THR B 381 1 8 HELIX 31 AD4 SER B 383 ASN B 390 1 8 HELIX 32 AD5 SER B 393 LEU B 406 1 14 HELIX 33 AD6 LEU B 407 GLU B 409 5 3 HELIX 34 AD7 THR B 419 ALA B 436 1 18 HELIX 35 AD8 THR B 437 SER B 440 5 4 HELIX 36 AD9 LYS B 441 THR B 455 1 15 HELIX 37 AE1 ASN B 468 LEU B 485 1 18 HELIX 38 AE2 SER B 486 LYS B 490 5 5 HELIX 39 AE3 PRO B 491 ARG B 516 1 26 HELIX 40 AE4 SER B 530 ILE B 542 1 13 HELIX 41 AE5 ILE B 542 VAL B 554 1 13 HELIX 42 AE6 ALA B 558 SER B 574 1 17 LINK NE2 HIS A 330 ZN ZN A 601 1555 1555 2.19 LINK OD2 ASP A 333 MG MG A 603 1555 1555 2.62 LINK NE2 HIS A 366 ZN ZN A 601 1555 1555 2.19 LINK OD2 ASP A 367 ZN ZN A 601 1555 1555 2.10 LINK OD1 ASP A 367 MG MG A 602 1555 1555 2.05 LINK OD1 ASN A 417 MG MG A 604 1555 4497 2.15 LINK OD2 ASP A 467 MG MG A 605 1555 1555 2.02 LINK OD2 ASP A 471 MG MG A 605 1555 1555 2.12 LINK OD1 ASP A 484 ZN ZN A 601 1555 1555 2.13 LINK ZN ZN A 601 O HOH A 756 1555 1555 2.06 LINK ZN ZN A 601 O HOH A 840 1555 1555 2.25 LINK MG MG A 602 O HOH A 756 1555 1555 2.10 LINK MG MG A 602 O HOH A 803 1555 1555 2.05 LINK MG MG A 602 O HOH A 857 1555 1555 2.16 LINK MG MG A 602 O HOH A 867 1555 1555 2.20 LINK MG MG A 602 O HOH A 933 1555 1555 2.11 LINK MG MG A 604 O HOH A 714 1555 1555 2.18 LINK MG MG A 604 O HOH A 839 1555 4597 2.02 LINK MG MG A 604 O HOH A 847 1555 4597 2.23 LINK MG MG A 605 O HOH A 779 1555 1555 2.18 LINK MG MG A 605 O HOH A 780 1555 3647 2.24 LINK MG MG A 605 O HOH A 814 1555 1555 2.21 LINK NE2 HIS B 330 ZN ZN B 601 1555 1555 2.16 LINK NE2 HIS B 366 ZN ZN B 601 1555 1555 2.22 LINK OD2 ASP B 367 ZN ZN B 601 1555 1555 2.09 LINK OD1 ASP B 367 MG MG B 602 1555 1555 2.05 LINK OD1 ASP B 484 ZN ZN B 601 1555 1555 2.15 LINK ZN ZN B 601 O HOH B 726 1555 1555 2.14 LINK ZN ZN B 601 O HOH B 838 1555 1555 2.29 LINK MG MG B 602 O HOH B 726 1555 1555 2.10 LINK MG MG B 602 O HOH B 758 1555 1555 2.12 LINK MG MG B 602 O HOH B 832 1555 1555 2.08 LINK MG MG B 602 O HOH B 848 1555 1555 2.16 LINK MG MG B 602 O HOH B 868 1555 1555 2.11 CISPEP 1 VAL A 257 LEU A 258 0 0.26 CISPEP 2 HIS A 555 PRO A 556 0 1.99 CISPEP 3 HIS B 555 PRO B 556 0 4.53 SITE 1 AC1 7 HIS A 330 HIS A 366 ASP A 367 ASP A 484 SITE 2 AC1 7 MG A 602 HOH A 756 HOH A 840 SITE 1 AC2 7 ASP A 367 ZN A 601 HOH A 756 HOH A 803 SITE 2 AC2 7 HOH A 857 HOH A 867 HOH A 933 SITE 1 AC3 5 TYR A 325 HIS A 330 ASP A 333 ASN A 487 SITE 2 AC3 5 TRP A 498 SITE 1 AC4 1 HOH A 714 SITE 1 AC5 6 ASP A 467 ASP A 471 HIS A 527 HOH A 779 SITE 2 AC5 6 HOH A 780 HOH A 814 SITE 1 AC6 16 TYR A 325 HIS A 326 MET A 439 ASN A 487 SITE 2 AC6 16 THR A 499 ILE A 502 PHE A 506 MET A 523 SITE 3 AC6 16 CYS A 524 GLN A 535 PHE A 538 HOH A 707 SITE 4 AC6 16 HOH A 757 HOH A 766 HOH A 819 HOH A 829 SITE 1 AC7 6 HIS B 330 HIS B 366 ASP B 367 ASP B 484 SITE 2 AC7 6 HOH B 726 HOH B 838 SITE 1 AC8 6 ASP B 367 HOH B 726 HOH B 758 HOH B 832 SITE 2 AC8 6 HOH B 848 HOH B 868 SITE 1 AC9 14 TYR B 325 SER B 374 ASN B 487 THR B 499 SITE 2 AC9 14 ILE B 502 PHE B 506 MET B 523 CYS B 524 SITE 3 AC9 14 GLN B 535 PHE B 538 HOH B 714 HOH B 772 SITE 4 AC9 14 HOH B 828 HOH B 863 CRYST1 64.531 98.717 119.623 90.00 90.00 90.00 P 21 21 21 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.015496 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010130 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008360 0.00000